There's a reason John Sheppard has the ATA gene. And that reason is Jack O'Neill. McKay/Sheppard first time, Jack/Daniel established, Sam/Radek first time, Hammond/Weir implied, implied Jack/John's mother-cheating.

Ancient intelligent carts. Established from part 2 onwards. Mostly McKay/Sheppard, but with other pairings, some of which have episodes and parts dedicated to them: Beckett/Zelenka, Lorne/Chuck, Cadman/O'Neill!Clone, Grodin/OFC (Lindstrom), Bates/Lindstrom, Weir/Paul Davis, implied Jack/Daniel.